Thermostatically Controlled Fan Confusion

Up until now I've had my hotend fan on constantly and just set it up to be thermostatically controlled. I have it hooked up to Fan 1 (not Fan0) and have M106 P1 T45 S255 H1 in my config.g. Now, when I manually enter the temperature, the fan turns on and off when it reaches and falls below 45deg, respectively. But when I start a print and it gets to the desired temp, the fan doesn't turn on until I stop the print (when it's over 45). Any ideas on what's happening?

PS: I tested a print as M106 P1 H-1. It was on at first, but turned off once the print started. Is it something in the slicer (I'm using Simplify3d)? I can't find anything that could override the fan control.